Zinc in the structure of Crystal Structure of Sulfolobus Shibatae Rna Polymerase in P21 Space Group (pdb 2y0s)

The binding sites of Zinc atom in the structure of Crystal Structure of Sulfolobus Shibatae Rna Polymerase in P21 Space Group (pdb code 2y0s). This binding sites where shown with 5.0 Angstroms radius around Zinc atom. The 2y0s structure was solved by M.WOJTAS, B.PERALTA, M.ONDIVIELA, M.MOGNI, S.D.BELL, N.G.A.ABRESCIA, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 29.9-3.8 Space group P1211 a (A) 129.330 b (A) 195.909 c (A) 212.451 alpha (°) 90.00 beta (°) 105.73 gamma (°) 90.00 Rfactor (%) 29.97 Rfree (%) 35.39 Zinc Binding Sites: Zinc binding site 1 out of 14 in 2y0s Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Zinc in the PDB 2y0s. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Gly50, A: Cys58, A: Thr60, A: Cys61, A: Gly62, A: Cys68, A: Pro69, A: His71, conact list: Atom Atom Distance (A) Zn CA A:Gly50 4.65 Zn CB A:Cys58 3.20 Zn SG A:Cys58 1.59 Zn CA A:Cys58 4.46 Zn CG2 A:Thr60 3.61 Zn N A:Cys61 4.43 Zn CB A:Cys61 3.82 Zn SG A:Cys61 1.99 Zn CA A:Cys61 4.76 Zn N A:Gly62 5.00 Zn O A:Cys68 2.64 Zn CB A:Cys68 3.14 Zn SG A:Cys68 1.99 Zn C A:Cys68 3.34 Zn CA A:Cys68 3.72 Zn O A:Pro69 4.91 Zn N A:Pro69 4.36 Zn C A:Pro69 4.90 Zn CA A:Pro69 4.88 Zn NE2 A:His71 1.93 Zn ND1 A:His71 3.94 Zn CD2 A:His71 2.81 Zn CE1 A:His71 2.92 Zn CG A:His71 3.92 interactive model: Zinc binding site 2 out of 14 in 2y0s Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Zinc in the PDB 2y0s. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Cys98, A: Arg100, A: Cys101, A: Gly102, A: Lys142, A: Gln144, A: Val145, A: Cys146, conact list: Atom Atom Distance (A) Zn O A:Cys98 3.99 Zn N A:Cys98 4.57 Zn CB A:Cys98 2.10 Zn SG A:Cys98 0.72 Zn C A:Cys98 4.04 Zn CA A:Cys98 3.48 Zn N A:Arg100 4.98 Zn C A:Arg100 4.78 Zn N A:Cys101 3.97 Zn CB A:Cys101 2.89 Zn SG A:Cys101 1.73 Zn C A:Cys101 4.89 Zn CA A:Cys101 4.06 Zn O A:Gly102 4.67 Zn N A:Gly102 4.81 Zn O A:Lys142 4.90 Zn N A:Gln144 4.69 Zn CB A:Gln144 4.69 Zn C A:Gln144 4.71 Zn CA A:Gln144 4.92 Zn O A:Val145 2.82 Zn N A:Val145 3.56 Zn CB A:Val145 4.53 Zn C A:Val145 3.29 Zn CG1 A:Val145 3.86 Zn CA A:Val145 3.91 Zn N A:Cys146 3.93 Zn CB A:Cys146 3.81 Zn SG A:Cys146 2.43 Zn CA A:Cys146 4.18 interactive model: Zinc binding site 3 out of 14 in 2y0s Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Zinc in the PDB 2y0s. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Cys1064, B: Gln1066, B: Cys1067, B: Tyr1069, B: Cys1082, B: Ile1084, B: Ser1089, conact list: Atom Atom Distance (A) Zn CB B:Cys1064 3.58 Zn SG B:Cys1064 2.01 Zn CA B:Cys1064 4.93 Zn CB B:Gln1066 4.74 Zn N B:Cys1067 4.02 Zn CB B:Cys1067 3.09 Zn SG B:Cys1067 1.87 Zn CA B:Cys1067 4.24 Zn O B:Tyr1069 4.92 Zn CB B:Cys1082 4.44 Zn SG B:Cys1082 3.01 Zn N B:Ile1084 4.33 Zn CB B:Ile1084 2.89 Zn CD1 B:Ile1084 4.17 Zn CG2 B:Ile1084 3.66 Zn C B:Ile1084 4.90 Zn CG1 B:Ile1084 2.73 Zn CA B:Ile1084 4.16 Zn OG B:Ser1089 4.40 interactive model: Zinc binding site 4 out of 14 in 2y0s Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Zinc in the PDB 2y0s. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Arg174, B: Gly527, B: His570, B: Val571, B: Asn572, B: Glu622, conact list: Atom Atom Distance (A) Zn CZ B:Arg174 4.82 Zn NH1 B:Arg174 4.26 Zn N B:Gly527 4.74 Zn NE2 B:His570 4.15 Zn CB B:His570 3.15 Zn ND1 B:His570 2.14 Zn CD2 B:His570 4.08 Zn C B:His570 4.81 Zn CE1 B:His570 3.14 Zn CG B:His570 2.93 Zn CA B:His570 4.27 Zn N B:Val571 4.91 Zn CB B:Asn572 4.51 Zn ND2 B:Asn572 3.17 Zn OD1 B:Asn572 2.13 Zn CG B:Asn572 2.99 Zn OE1 B:Glu622 3.52 Zn CD B:Glu622 4.47 Zn CG B:Glu622 4.89 interactive model: Zinc binding site 5 out of 14 in 2y0s Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Zinc in the PDB 2y0s. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Asp418, B: Arg419, B: Thr420, conact list: Atom Atom Distance (A) Zn CB B:Asp418 4.79 Zn OD2 B:Asp418 3.02 Zn OD1 B:Asp418 4.89 Zn CG B:Asp418 4.07 Zn N B:Arg419 4.89 Zn C B:Arg419 4.70 Zn N B:Thr420 3.76 Zn CB B:Thr420 3.35 Zn CG2 B:Thr420 4.41 Zn OG1 B:Thr420 2.10 Zn CA B:Thr420 3.57 interactive model: Zinc binding site 6 out of 14 in 2y0s Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Zinc in the PDB 2y0s. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: N: Cys7, N: Thr9, N: Cys10, N: Gly11, N: Ser12, N: Cys44, N: Cys45, N: Arg46, N: Arg47, conact list: Atom Atom Distance (A) Zn CB N:Cys7 3.37 Zn SG N:Cys7 2.31 Zn CA N:Cys7 4.78 Zn N N:Thr9 4.70 Zn CB N:Thr9 4.22 Zn OG1 N:Thr9 5.00 Zn C N:Thr9 4.55 Zn CA N:Thr9 4.71 Zn N N:Cys10 3.46 Zn CB N:Cys10 3.09 Zn SG N:Cys10 2.01 Zn C N:Cys10 4.88 Zn CA N:Cys10 3.88 Zn N N:Gly11 4.76 Zn OG N:Ser12 4.95 Zn O N:Cys44 3.65 Zn N N:Cys44 4.28 Zn CB N:Cys44 3.14 Zn SG N:Cys44 2.12 Zn C N:Cys44 2.91 Zn CA N:Cys44 3.57 Zn N N:Cys45 2.34 Zn CB N:Cys45 2.78 Zn SG N:Cys45 2.08 Zn C N:Cys45 4.22 Zn CA N:Cys45 2.72 Zn N N:Arg46 4.86 Zn NH2 N:Arg47 4.75 interactive model: Zinc binding site 7 out of 14 in 2y0s Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Zinc in the PDB 2y0s. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: O: Cys7, O: Thr9, O: Cys10, O: Gly11, O: Cys44, O: Cys45, O: Arg46, O: Arg47, conact list: Atom Atom Distance (A) Zn CB O:Cys7 3.31 Zn SG O:Cys7 2.23 Zn CA O:Cys7 4.72 Zn N O:Thr9 4.72 Zn CB O:Thr9 4.27 Zn C O:Thr9 4.66 Zn CA O:Thr9 4.78 Zn N O:Cys10 3.60 Zn CB O:Cys10 3.33 Zn SG O:Cys10 2.19 Zn CA O:Cys10 4.08 Zn N O:Gly11 4.89 Zn O O:Cys44 3.45 Zn N O:Cys44 4.21 Zn CB O:Cys44 3.08 Zn SG O:Cys44 2.13 Zn C O:Cys44 2.77 Zn CA O:Cys44 3.47 Zn O O:Cys45 4.83 Zn N O:Cys45 2.16 Zn CB O:Cys45 2.72 Zn SG O:Cys45 2.16 Zn C O:Cys45 4.01 Zn CA O:Cys45 2.51 Zn N O:Arg46 4.67 Zn NH2 O:Arg47 4.63 interactive model: Zinc binding site 8 out of 14 in 2y0s Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Zinc in the PDB 2y0s. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: P: Cys9, P: Trp10, P: Thr12, P: Thr14, P: Cys26, P: Pro27, P: Tyr28, P: Cys29, conact list: Atom Atom Distance (A) Zn N P:Cys9 4.66 Zn CB P:Cys9 2.36 Zn SG P:Cys9 2.01 Zn C P:Cys9 4.72 Zn CA P:Cys9 3.91 Zn N P:Trp10 4.80 Zn O P:Trp10 4.52 Zn O P:Thr12 3.35 Zn N P:Thr12 4.59 Zn CB P:Thr12 3.39 Zn CG2 P:Thr12 4.37 Zn OG1 P:Thr12 2.05 Zn C P:Thr12 4.19 Zn CA P:Thr12 4.24 Zn CB P:Thr14 4.85 Zn OG1 P:Thr14 4.63 Zn CB P:Cys26 3.93 Zn SG P:Cys26 2.31 Zn O P:Pro27 4.70 Zn O P:Tyr28 4.27 Zn C P:Tyr28 4.93 Zn CB P:Cys29 3.58 Zn SG P:Cys29 1.85 Zn CA P:Cys29 4.51 interactive model: Zinc binding site 9 out of 14 in 2y0s Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Zinc in the PDB 2y0s. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: R: Cys1064, R: Gln1066, R: Cys1067, R: Cys1082, R: Ile1084, R: Ser1089, conact list: Atom Atom Distance (A) Zn CB R:Cys1064 3.70 Zn SG R:Cys1064 2.04 Zn CA R:Cys1064 4.91 Zn N R:Gln1066 4.87 Zn OE1 R:Gln1066 4.53 Zn CB R:Gln1066 4.35 Zn C R:Gln1066 4.86 Zn CA R:Gln1066 4.95 Zn N R:Cys1067 3.97 Zn CB R:Cys1067 3.39 Zn SG R:Cys1067 2.11 Zn CA R:Cys1067 4.34 Zn CB R:Cys1082 4.67 Zn SG R:Cys1082 3.16 Zn N R:Ile1084 4.68 Zn CB R:Ile1084 3.07 Zn CD1 R:Ile1084 4.58 Zn CG2 R:Ile1084 3.67 Zn C R:Ile1084 4.95 Zn CG1 R:Ile1084 3.13 Zn CA R:Ile1084 4.38 Zn CB R:Ser1089 4.99 Zn OG R:Ser1089 3.85 interactive model: Zinc binding site 10 out of 14 in 2y0s Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 10 of Zinc in the PDB 2y0s. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: R: Arg174, R: Gly527, R: His570, R: Asn572, R: Glu622, conact list: Atom Atom Distance (A) Zn CZ R:Arg174 4.76 Zn NH1 R:Arg174 4.19 Zn N R:Gly527 4.73 Zn NE2 R:His570 4.16 Zn CB R:His570 3.24 Zn ND1 R:His570 2.10 Zn CD2 R:His570 4.12 Zn C R:His570 4.90 Zn CE1 R:His570 3.12 Zn CG R:His570 2.98 Zn CA R:His570 4.31 Zn CB R:Asn572 4.50 Zn ND2 R:Asn572 3.15 Zn OD1 R:Asn572 2.13 Zn CG R:Asn572 2.98 Zn OE1 R:Glu622 3.46 Zn CD R:Glu622 4.44 Zn CG R:Glu622 4.87 interactive model: Zinc binding site 11 out of 14 in 2y0s Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 11 of Zinc in the PDB 2y0s. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: R: Asp418, R: Arg419, R: Thr420, R: Arg694, conact list: Atom Atom Distance (A) Zn CB R:Asp418 4.79 Zn OD2 R:Asp418 3.37 Zn CG R:Asp418 4.34 Zn CA R:Asp418 4.92 Zn N R:Arg419 4.90 Zn N R:Thr420 4.31 Zn CB R:Thr420 4.20 Zn OG1 R:Thr420 3.02 Zn CA R:Thr420 4.27 Zn CD R:Arg694 4.97 Zn CG R:Arg694 4.99 interactive model: Zinc binding site 12 out of 14 in 2y0s Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 12 of Zinc in the PDB 2y0s. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: W: Gly50, W: Cys58, W: Thr60, W: Cys61, W: Gly62, W: Cys68, W: Pro69, W: His71, conact list: Atom Atom Distance (A) Zn CA W:Gly50 4.81 Zn CB W:Cys58 3.26 Zn SG W:Cys58 1.67 Zn CA W:Cys58 4.50 Zn CB W:Thr60 4.95 Zn CG2 W:Thr60 3.53 Zn C W:Thr60 4.94 Zn N W:Cys61 4.34 Zn CB W:Cys61 3.64 Zn SG W:Cys61 1.84 Zn CA W:Cys61 4.60 Zn N W:Gly62 4.93 Zn O W:Cys68 2.78 Zn CB W:Cys68 3.26 Zn SG W:Cys68 1.99 Zn C W:Cys68 3.43 Zn CA W:Cys68 3.78 Zn O W:Pro69 4.91 Zn N W:Pro69 4.42 Zn C W:Pro69 4.95 Zn CA W:Pro69 4.93 Zn NE2 W:His71 1.88 Zn ND1 W:His71 3.82 Zn CD2 W:His71 2.83 Zn CE1 W:His71 2.78 Zn CG W:His71 3.88 interactive model: Zinc binding site 13 out of 14 in 2y0s Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 13 of Zinc in the PDB 2y0s. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: W: Cys98, W: Arg99, W: Arg100, W: Cys101, W: Lys142, W: Gln144, W: Val145, W: Cys146, conact list: Atom Atom Distance (A) Zn O W:Cys98 3.53 Zn N W:Cys98 4.93 Zn CB W:Cys98 2.67 Zn SG W:Cys98 1.62 Zn C W:Cys98 3.87 Zn CA W:Cys98 3.66 Zn N W:Arg99 4.96 Zn N W:Arg100 4.57 Zn CB W:Arg100 4.80 Zn C W:Arg100 4.56 Zn CA W:Arg100 4.93 Zn N W:Cys101 4.00 Zn CB W:Cys101 3.11 Zn SG W:Cys101 1.32 Zn CA W:Cys101 4.20 Zn O W:Lys142 4.95 Zn C W:Gln144 4.72 Zn O W:Val145 2.04 Zn N W:Val145 3.46 Zn CB W:Val145 4.05 Zn CG2 W:Val145 4.81 Zn C W:Val145 2.68 Zn CG1 W:Val145 3.45 Zn CA W:Val145 3.51 Zn N W:Cys146 3.42 Zn CB W:Cys146 3.26 Zn SG W:Cys146 1.64 Zn CA W:Cys146 3.63 interactive model: Zinc binding site 14 out of 14 in 2y0s Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 14 of Zinc in the PDB 2y0s. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: X: Cys9, X: Trp10, X: Thr12, X: Thr14, X: Cys26, X: Pro27, X: Tyr28, X: Cys29, conact list: Atom Atom Distance (A) Zn N X:Cys9 4.64 Zn CB X:Cys9 2.40 Zn SG X:Cys9 2.13 Zn C X:Cys9 4.79 Zn CA X:Cys9 3.95 Zn N X:Trp10 4.85 Zn O X:Trp10 4.57 Zn O X:Thr12 3.30 Zn N X:Thr12 4.58 Zn CB X:Thr12 3.35 Zn CG2 X:Thr12 4.35 Zn OG1 X:Thr12 2.03 Zn C X:Thr12 4.16 Zn CA X:Thr12 4.22 Zn CB X:Thr14 4.76 Zn OG1 X:Thr14 4.54 Zn CB X:Cys26 3.98 Zn SG X:Cys26 2.33 Zn O X:Pro27 4.71 Zn O X:Tyr28 4.29 Zn C X:Tyr28 4.96 Zn CB X:Cys29 3.64 Zn SG X:Cys29 1.90 Zn CA X:Cys29 4.59 interactive model: